Selenoprotein synthesis in archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion

Selenocysteine is encoded by a UGA codon in all organisms that synthesise selenoproteins. This codon is specified as a selenocysteine codon by an mRNA secondary structure, which is located immediately 3' of the UGA in the reading frame of selenoprotein genes in Gram-negative bacteria, whereas it is located in the 3' untranslated region of eukaryal selenoprotein genes. The location and the structure of a similar mRNA signal in archaea has so far not been determined. Seven selenoproteins were identified for the archaeon Methanococcus jannaschii by labelling with 75Se and by SDS/polyacrylamide electrophoresis. Their size could be correlated with open reading frames possessing internal UGA codons from the total genomic sequence. One of the open reading frames, that of the VhuD subunit of a hydrogenase, possesses two UGA codons and appears to code for a selenoprotein with two selenocysteine residues. A strongly conserved mRNA element was identified that is exclusively linked to selenoprotein genes. It is located in the 3' untranslated region in six of the mRNAs and in the 5' untranslated region of the fdhA mRNA. This element, which is present in the 3' non-translated region of two selenoprotein mRNAs from Methanococcus voltae, is proposed to act in decoding of the UGA with selenocysteine.

Development of genetic approaches for the methane-producing archaebacterium Methanococcus maripaludis

Methanococcus maripaludis is a strict anaerobe that utilizes H2 or formate as an electron donor for CO2 reduction to methane. Recent progress in development of genetic systems in this archaebacterium makes it an excellent model system for molecular and biochemical studies. This progress includes development of methods for growth on solid medium, enriching auxotrophic mutants, efficient transformation, and random insertional inactivation of genes. Genetic markers for both puromycin and neomycin resistance are available. Lastly, a shuttle vector has been constructed from a cryptic methanococcal plasmid. These technical advances made it possible to utilize genetic approaches for the study of autotrophic CO2 assimilation in methanococci.

Phylogeny and taxonomy of mesophilic Methanococcus spp. and comparison of rRNA, DNA hybridization, and phenotypic methods

The phylogeny and taxonomy of the mesophilic methane-producing archaea of the order Methanococcales were examined by DNA relatedness, 16S rRNA sequence analysis, cellular protein patterns, and phenotypic methods. The mesophilic species Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltaei, and "Methanococcus aeolicus" formed a deep group with 5 to 30% DNA relatedness and 92 to 96% 16S rRNA sequence similarity. Twenty-two additional isolates and Methanococcus deltae were similar to the type strain of either M. voltaei or M. maripaludis. Two isolates, strains A2 and A3, exhibited 37% DNA relatedness and 99.2% 16S rRNA sequence similarity to M. voltaei PS(T) (T = type strain). In the absence of phenotypic differences, these organisms were assigned to M. voltaei. Similarly, four autotrophic isolates, strains C5, C6, C7, and C8, exhibited 54 to 69% DNA relatedness and 99.2% 16S rRNA sequence similarity to M. maripaludis JJT and were assigned to M. Maripaludis. While these isolates were sufficiently genetically diverse to justify classification in novel species, few differences were apparent in the phenotypic properties available for measurement. Thus, the phenotypic properties of these lithotrophic archaea were highly conserved and poor indicators of genetic diversity. Partial sequencing of about 200 bases of both the 16S and 23S rRNAs of the isolates demonstrated allelic diversity within methanococcal species. This allelic diversity did not correlate with diversity measured by DNA relatedness, cellular protein pattern, and other methods. Similarly, antisera to whole cells of the type strains did not cross-react strongly to whole cells of strains that were genetically similar, and serological cross-reactivity was not a useful taxonomic method for methanococci. Lastly, on the basis of the results of 16S rRNA sequence analyses and biochemical data, the ancestor of the mesophilic methanococci may have been an autotrophic thermophile.

Isolation and characterization of insertional mutations in flagellin genes in the archaeon Methanococcus voltae

Methanococcus voltae is a flagellated member of the Domain Archaea that has four flagellin genes arranged in two transcriptional units. One transcriptional unit encodes only flaA while the second is a multi-cistronic unit encoding three flagellin genes (flaB1, flaB2, and flaB3) as well as at least seven other open reading frames downstream. The polymerase chain reaction was used to amplify an internal fragment of the flaA gene which was subsequently cloned into an insertion vector developed for M. voltae. Transformation of protoplasts with this vector led to the isolation of mutant strains that had insertions in flaA or flaB2. Mutant strains carrying insertions in flaA had flagelia that were similar to wild-type cells in both number and appearance when viewed using the electron microscope. In addition, some of these mutant strains had profiles identical to the wild type in immunoblots developed with antisera raised against the 31 kDa flagellin of M. voltae. All flaA mutant strains and the wild-type cells showed immuno-cross-reactive bands at 33 and 31 kDa (corresponding to purified flagellins) as well as at 18 kDa. Some flaA mutant strains also showed an immuno-cross-reactive band at 27 kDa which probably represents a truncated flagellin produced by the insertion vector. However, both types of flaA mutant strains were less motile than the wild type in semi-swarm plate experiments. The mutant strain with an insertion in flaB2 was non-flagellated when examined by electron microscopy and it was non-motile in semi-swarm plate experiments. It represents the first structural mutant strain isolated in a methanogen. This mutant strain lacked the 33, 31, and 18 kDa immuno-cross-reactive bands observed in the wild type and flaA mutant strains, and instead had a novel band at 20 kDa. This band may represent an unmodified flagellin which still has an attached leader peptide. If so, then one of the downstream genes in the multi-cistronic transcriptional unit may encode a leader peptidase for the flagellin system.

The translation product of the presumptive Thermococcus celer TATA-binding protein sequence is a transcription factor related in structure and function to Methanococcus transcription factor B

A gene for a putative homolog of TATA-binding protein (TBP) from Thermococcus celer has been expressed in Escherichia coli, and the function of the purified recombinant protein was studied in a Methanococcus-derived cell-free transcription system. Thermococcus TBP can replace archaeal transcription factor B (aTFB) in cell-free transcription reactions. This transcriptional activation is TATA box-dependent and occurs both on tRNA(Val) and protein-encoding genes as templates indicating that Thermococcus TBP is a general transcription factor. Antibodies raised against Thermococcus TBP bind to Methanococcus aTFB and inhibit a TFB activity. These findings demonstrate that Thermococcus TBP (like eucaryal TBPs) can direct specific transcription from TATA boxes.

Biosynthesis of (7-mercaptoheptanoyl)threonine phosphate

The biosynthesis of (7-mercaptoheptanoyl)threonine phosphate (HS-HTP) has been studied in the methanogenic bacteria Methanococcus volta and Methanosarcina thermophila. Growth of these cells in medium containing [7,7-2H2]-7-mercaptoheptanoic acid, [3,4,4,4-threonine-2H4]-N-(7-mercaptoheptanoyl)threonine, [7,7-2H2]-N-(7-mercaptoheptanoyl)threonine, or DL-[3,4,4,4-2H4]threonine led to the generation of labeled HS-HTP containing a portion of the molecules with the same number of deuteriums as the precursor molecule. This result indicated that each of these labeled molecules can serve as a precursor for the biosynthesis of HS-HTP. Cell-free extracts of these methanogens were shown to carry out the ATP-dependent phosphorylation of N-(7-mercaptoheptanoyl)threonine to HS-HTP. These observations indicate that the biosynthesis of HS-HTP involves the coupling of mercaptoheptanoic acid with threonine to form (7-mercaptoheptanoyl)threonine, which is then phosphorylated to HS-HTP.

Biotransformation of 2,4,6-trinitrotoluene (TNT) by a Methanococcus sp. (strain B) isolated from a lake sediment

A mesophilic, irregular coccoid methanogen, which shows close resemblance to Methanococcus sp., was isolated from a sediment sample of St. Joseph Lake located in the University of Notre Dame campus. Formate or hydrogen plus carbon dioxide served as substrate for methanogenesis in a mineral salt medium. This organism was studied for its ability to metabolize 2,4,6-trinitrotoluene (TNT). The result showed that this isolate could transform 100 ppm of TNT within 40-60 days of incubation at 30 degrees C. The main intermediate produced was 2,4-diamino-6-nitrotoluene. The TNT transformation rates were higher in cells grown in hydrogen plus carbon dioxide than in cells grown in formate. The isolate did not use acetate and methanol as sole source of carbon and energy. The organism had an optimal pH range of 6.8-7.2. The optimal growth conditions for this isolate are described.

mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing

Cells from the early exponential growth phase of cultures of the methanogenic archaeon Methanococcus vannielii have been shown to contain c. 180 transcripts of the mcrBDCGA (mcr) operon, c. 100 transcripts of the MvaL1,L10,L12 (Mva) operon, c. 8 transcripts of the argG gene and c. 1 transcript of the secY gene. These values decreased to c. 50 mcr transcripts, c. 30 Mva transcripts, c. 3 argG transcripts and < 1 secY transcript per cell as the cultures entered the stationary phase of growth. Addition of bromo-ethanesulphonate (BES) or removal of H2 inhibited growth and RNA synthesis in vivo and, at 37 degrees C in the presence of BES, the half-lives of the mcr, Mva, argG and secY transcripts were found to be 15 min, 30 min, 57 min and 7 min, respectively. Addition of puromycin, pseudomonic acid or virginiamycin also inhibited growth but did not inhibit transcription. In the presence of puromycin the half-lives of the mcr and Mva transcripts increased c. 4.6-fold and c. 3.5-fold, respectively, and there was a net accumulation of the Mva transcript. Addition of pseudomonic acid or virginiamycin also increased the half-life of the Mva transcript and also resulted in the accumulation of a second, shorter Mva transcript but did not increase the half-life of the mcr transcript. Transcription of the mcr operon was not stimulated by partial inhibition of methanogenesis.

Pathway of glycogen metabolism in Methanococcus maripaludis

Methanococcus maripaludis, a facultatively autotrophic archaebacterium that grows with H2 or formate as the electron donor, does not assimilate sugars and other complex organic substrates. However, glycogen is biosynthesized intracellularly and commonly reaches values of 0.34% of the cellular dry weight in the early stationary phase. To determine the pathway of glycogen catabolism, specific enzymes of sugar metabolism were assayed in cell extracts. The following enzymes were found (specific activity in milliunits per milligram of protein): glycogen phosphorylase, 4.4; phosphoglucomutase, 10; glucose-6-phosphate isomerase, 9; 6-phosphofructokinase, 5.6, fructose-1,6-bisphosphatase, 10; fructose-1,6-bisphosphate aldolase, 4.2; triosephosphate isomerase, 44; glyceraldehyde-3-phosphate dehydrogenase, 26; phosphoglycerate kinase, 20; phosphoglycerate mutase, 78; enolase, 107; and pyruvate kinase, 4.0. Glyceraldehyde-3-phosphate dehydrogenase was NADP+ dependent, and the pyruvate kinase required MnCl2. The 6-phosphofructokinase had an unusually low pH optimum of 6.0. Four nonoxidative pentose-biosynthetic enzymes were found (specific activity in milliunits per milligram of protein): transketolase, 12; transaldolase, 24; ribulose-5-phosphate-3-epimerase, 55; and ribulose-5-phosphate isomerase, 100. However, the key enzymes of the oxidative pentose phosphate pathway, the reductive pentose phosphate pathway, and the classical and modified Entner-Duodoroff pathways were not detected. Thus, glycogen appears to be catabolized by the Embden-Meyerhoff-Parnas pathway. This result is in striking contrast to the nonmethanogenic archaebacteria that have been examined, among which the Entner-Doudoroff pathway is common. A dithiothreitol-specific NADP(+)-reducing activity was also found (8.5 mU/mg of protein). Other thiol compounds, such as cysteine hydrochloride, reduced glutathione, and 2-mercaptoethanesulfonic acid, did not replace dithiothreitol for this activity. The physiological significance of this activity is not known.

Purification and characterization of a general transcription factor, aTFB, from the archaeon Methanococcus thermolithotrophicus

We have recently shown that cell-free transcription of homologous templates from the archaeon Methanococcus thermolithotrophicus requires an archaeal transcription factor (aTFA) that separated from the RNA polymerase during phosphocellulose chromatography. We report here the identification and extensive purification of a second activity, aTFB, required for in vitro transcription. This activity copurified with RNA polymerase during initial chromatographic steps but was positively identified as a distinct transcription factor after Superdex 200 sizing chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the intensity of a M(r) = 28,000 polypeptide in silver-stained gels is correlated with transcription factor activity. The same polypeptide, when eluted from a denaturing polyacrylamide gel and subsequently renatured, showed the functional properties of the transcription factor. In conjunction with gel filtration and sedimentation studies, which indicated a molecular mass of 54,000 Da for the native protein, these results suggested that aTFB is a dimer with polypeptide chains of identical molecular mass. Functional studies with highly purified aTFB demonstrated that it is a general factor required for transcription of genes encoding tRNA and proteins.

Purine metabolism in Methanococcus vannielii

Methanococcus vannielii is capable of degrading purines to the extent that each of these purines may serve as the sole nitrogen source for growth. Results presented here demonstrate that purine degradation by M. vannielii is accomplished by a route similar to that described for clostridia. Various characteristics of the purine-degrading pathway of M. vannielii are described. Additionally, it is shown that M. vannielii does not extensively degrade exogenously supplied guanine if that compound is present at levels near or lower than those required to supply the cellular guanine requirement. Under those conditions, M. vannielii incorporates the intact guanine molecule into its guanine nucleotide pool. The benefits of a purine-degrading pathway to methanogens are discussed.

Identification of the mcrC gene product in Methanococcus vannielii

The polypeptide encoded by the mcrC gene has been identified in Methanococcus vannielii by immunoblotting using rabbit antibodies raised against the product of a lacZ-mcrC gene fusion synthesized and purified from Escherichia coli. The mcrC gene product (gpmcrC) was located in both the supernatant and pellet fractions after centrifugation of Mc. vannielii cell extracts for 2 h at 100,000 x g. When anaerobic reducing conditions were maintained during purification, gpmcrC co-sedimented through sucrose gradients to the same position as molecules of the methyl coenzyme M reductase holoenzyme (approx. 300 kDa). This co-sedimentation was lost under aerobic, nonreducing conditions.

Reductive dechlorination of 1,2-dichloroethane and chloroethane by cell suspensions of methanogenic bacteria

Concentrated cell suspensions of methanogenic bacteria reductively dechlorinated 1,2-dichloroethane via two reaction-mechanisms: a dihalo-elimination yielding ethylene and two hydrogenolysis reactions yielding chloroethane and ethane, consecutively. The transformation of chloroethane to ethane was inhibited by 1,2-dichloroethane. Stimulation of methanogenesis caused an increase in the amount of dechlorination products formed, whereas the opposite was found when methane formation was inhibited. Cells of Methanosarcina barkeri grown on H2/CO2 converted 1,2-dichloroethane and chloroethane at higher rates than acetate or methanol grown cells.